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Research Skills

Bioinformatics
Statistics
Cell culture
Molecular Biology
Feild work

Main

Agneesh Barua

I am a graduate student at the Okinawa Institute of Science and Technology Graduate University (OIST). The main focus of my PhD is evolutionary genetics of complex traits. I use quantitative genetics, phylogenetic comparative methods, genomics, transcriptomics, and network approaches to understand the genetic basis of complex trait evolution.

Education

PhD. Candidate

Okinawa Institute of Science and Technology Graduate University

Okinawa, Japan

current - 2017

  • Currently working on the origin of extra-cellular RNA in snake venom.

Msc Genetics

University of Calcutta

Kolkata, India

2015 - 2013

  • Thesis: Role of P16/CDKN2A in Glioma: A Molecular Study.

BSc(H) Zoology

University of Delhi

New Delhi, India

2013 - 2010

  • Special undergraduate research: Antifungal activity of Phyto-extracts of Piper longum, Aloe vera, and Withania somnifera against human fungal opportunistic pathogen Candida albicans.

Research Experience

Rotation Student

Okinawa Institute of Science and Technology Graduate University

Okinawa, Japan

2017 - 2016

  • Bio/Micro/Nano fuidcs Unit, Prof Amy Shen.
  • Oncology-Cell signalling Unit, Prof. Tadashi Yamamoto.
  • Project- Developing a microfluidic model to study cancer metastasis.
  • Role- Involved in identifying a suitable device that could be used to grow various mammalian cells and mimic the tumor-vascular tissue interface, followed by testing the effect of growth factors on the migration of mammalian breast cancer cells.
  • Achievements- Successfully developed a model system that could be used to observe changes in migration potential of cells exposed to different growth factors. Received A grade for both rotation projects.

Research Intern

Ecology and Evolution Unit, Okinawa Institute of Science and Technology Graduate University

Okinawa, Japan

2016 - 2016

  • Project- Characterising the evolutionary forces behind rapid evolution of snake venom genes.
  • Role- Gene annotation of newly sequenced Prothrobothrops mucrosqamatus genome, developing a visualization of transcriptional network using d3, mapping out sequence variants on protein structure using PyMol. 
  • Achievements- Developed skill sets in evolutionary biology, molecular evolution, bioinformatics, programming. Internship project was published with me as a co-author.

Project Fellow

National Institute of Mental Health and Neuroscience (NIMHANS)

Bangalore, India

2015 - 2015

  • Project-Using 2-D-Glucose (2-DG) as an adjuvant to supplement treatment by Temozolomide, in high grade glioma.
  • Role- Used various techniques in Cell Culture,  cytotoxicology, Immunocytochemistry to study the effects 2-DG had on glioma cells U87.
  • Achievement- Developed skill sets in Cell culture, Immunocytochemistry, cytotoxicology. Contributed to the development of a new assay based on Acridine Orange dye treatments to visualize and determine cell damage due to radiation. 

Project Assistant

National Institute of Mental Health and Neuroscience (NIMHANS)

Bangalore, India

2015 - 2014

  • Project- Molecular genetics of the role of P16/CDKN2A in Glioma
  • Role- Collection of blood samples from patient wards, and glioma tissue collection from  operating theaters.  Carry out DNA extractions, Bisulphide conversion of DNA, MS-PCR, Multiplex PCR.
  • Achievements- Gained experience and skills in molecular biology techniques. Both thesis and thesis presentation were awarded an O (Outstanding) grade.

Innovation Project Fellow

Delhi University and Jawarharlal Nehru University

New Delhi, India

2013 - 2012

  • Project- Antifungal activity of Phyto-extracts of Piper longum, Aloe vera, and Withania somnifera against human fungal opportunistic pathogen Candida albicans.
  • Role- Carried out fungal culture, preparation of plant extracts, and drug assays like MIC, Spot assay, and disc diffusion, also carried out GCMS analysis of plant extracts.
  • Achievements- Being selected as an Innovation Project Researcher involved writing a research proposal that was screened  by a committee of  5 professors. Over 100 candidates were involved in the process. 10 were selected.  Project was published in the Delhi University Journal of Undergraduate Research.

Publications

The parallel origins of vertebrate venom

Agneesh Barua, Ivan Koludarov, Alexander Mikheyev

N/A

2021

An ancient, conserved gene regulatory network led to the rise of oral venom systems

Agneesh Barua & Alexander Mikheyev

N/A

2021

Toxin expression in snake venom evolves rapidly with constant shifts in evolutionary rates

Agneesh Barua & Alexander Mikheyev

N/A

2020

Many options, few solutions: Over 60 my snakes converged on a few optimal venom formulations

Agneesh Barua & Alexander Mikheyev

N/A

2019

Population genomic analysis of a pitviper reveals microevolutionary forces underlying venom chemistry

SD Aird, J Arora, A Barua, L Qiu, K Terada, AS Mikheyev

N/A

2017

Antifungal activity of phyto-extracts of Piper longum, Aloe vera, and Withania somnifera against human fungal opportunistic pathogen Candida albicans

H Kaur, RR Goyal, A Bhattacharya, R Gupta, A Barua, … T Prasad

N/A

2015

Selected Press

Recommended article

Faculty Opinions

N/A

2021

Could humans ever be venomous?

Live Science

N/A

2021

Snake venom evolved in fits and spurts

PNAS Front Matter

N/A

2020

Venom and the mystery of evolution

Asahi Shimbun (Japanese only)

N/A

2020

  • Special feature highlighting my journey as a PhD student who uses venom to solve the mysteris of evolution.
  • Asahi Shimbun is the second largest circulating newspaper in the world.
  • https://globe.asahi.com/article/13581404

Snakes; The best bartenders in the Animal Kingdom?

OIST media release

N/A

2019

Academic Talks

Oxford Venoms and Toxins Conference (Online)

Toxin expression in snake venom evolves rapidly with constant shifts in evolutionary rates

Oxford, England

2020

European Society for Evolutionary Biolgy

Many options, few solutions: Over 60 my snakes converged on a few optimal venom formulations

Turku, Finalnd

2019

Gordon Conference on Venom Evolution , Function, and Biomedical Applications

Many options, few solutions: Over 60 my snakes converged on a few optimal venom formulations

Vermont, USA

2018

OIST internal seminar series

Many options, few solutions: Over 60 my snakes converged on a few optimal venom formulations

Okinawa, Japan

2018

Awards

Society membership

The American Society of Microbiology

N/A

2014 - 2013

  • Won a society membership by placing 1st in an inter-department Power-Point presentation contest.

Best Essay

The Acharya Prafulla Chandra Ray Memorial Science Forum. Calcutta University.

N/A

2013

  • Awarded 1st prize for best essay on entitled: Science and Society.

Innovation Project Fellow

Delhi University and Jawarharlal Nehru University

N/A

2012

  • Awarded a 12 month fellowship that covered stipend.

Teaching

Mini-course on Phylogentic Comparative Methods

OIST

Okinawa, Japan

2020

  • Gave a lecture on the importance and utility of phylogenetic comparative methods.
  • Graduate level class.

Ryukyu University Invited Lecture

Ryukyu University

Okinawa, Japan

2020

  • Was invited for a special lecture to 1st year undergrad students.
  • Lecture was on the origin of life in the ocean.
  • Undergraduate level class

Mini-course on quantitative genetics

OIST

Okinawa, Japan

2019 - 2017

  • TA and lectured on the Animal Model in quantitative genetics, and mixed models.
  • Graduate level class.

OIST Science Challenge

OIST

Okinawa, Japan

2019

  • Gave a lecture on Phylogenetics and how gene trees can teach us about about the history of animals.
  • Undergraduate level class.

Term course on Introduction to Molecular Biology

OIST

Okinawa, Japan

2018 - 2017

  • TA and lectured on a course introducing key concepts in molecular biology meant for non-biologists.
  • Undergraduate level class.

Professional Development

Academic Officer

OIST Student Council 2020

N/A

2021 - 2020

  • Was elected academic officer of the OIST student assembly.
  • Worked closely with different departments within the administration including Graduate School, Presidents Office, and Board of Governors/Councilors.
  • Worked with graduate school to formulize Student’s Code of Conduct and Academic Course Streams.

Organizer/Committee member

TEDxOIST

N/A

2018 - 2017

  • Organized the first TEDx event at my university in 2017.
  • Success of the first event was commemorated by a larger event the following year where I was a part of the advisory committee.

Conservation efforts

Fishing Cat Convervation Alliance

West Bengal, India

2011